BMP6 p.Leu293=
c.877T>C · rs144129356 · VCV3053293
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.598%, afr)
Conditions
1
BMP6-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3.4, phastCons 0.002 |
| Overall | ||
| CADD | 2.554 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.598%
African / African-American · 449/75,022 alleles
Filtering AF
0.553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.535%
Overall
0.0297%
479/1,614,120 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.598% | 167 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,906 |
| Admixed American | 0.015% | 6,669 |
| European (non-Finnish) | 0.000424% | 236,004 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BMP6
- Protein
- p.Leu293=
- Coding
- c.877T>C
- MANE Select
- NM_001718
- dbSNP
- rs144129356
- Type
- single nucleotide variant
- Location
- chr6:7861470 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 69.74 · 5 PDB
- Residue 293
- a UniProt-annotated variant site (in io; associated with disease susceptibility)
Disease context
BMP6-related disorder
Similar variants
- BMP6 c.1392+7T>G Likely benign same condition
- BMP6 c.665-3T>C Likely benign same condition
- BMP6 p.Ala189= Likely benign same condition
- BMP6 p.Ala189Thr Benign same condition
- BMP6 p.Ala212= Benign same condition
- BMP6 p.Ala343= Benign same condition
- BMP6 p.Arg28Gln Benign same condition
- BMP6 p.Arg396= Likely benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bmp6-p-leu293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown